Our objective is to provide the scientific community with a consistent, robust information environment for describing, sharing, integrating and comparing the functional roles of genes, proteins and functional RNAs within and across all organisms. The Gene Ontology (GO) Consortium is an international collaboration of model organism database and genome annotation groups who have joined together to establish standards for describing genomes and gene products and to provide tools and support for the consistent application of these standards for functional annotations that facilitate and enable biological research. The GO provides specific classifications including well-defined, biologically descriptive terms that are organized into specialization and part-of hierarchies for the domains of genome feature, molecular function, biological process and cellular component. The GO classifications are independent of any particular technology, an uncoupling of terminology from technology that encourages application of these semantic standards by organism annotation groups that utilize a wide range of technical environments. The GO has been widely adopted and used for representation of complex biological information for model organism genomes, and is increasingly used for the functional annotation of emerging genomes. With the increased use of the GO, the Consortium must actively work to ensure both the accuracy of the ontologies as well as consistency and quality of annotations so that these resources may be reliably used to draw inferences and make biological predictions. We will do so by focusing on four key aims: 1) We will maintain logically rigorous and biologically precise ontologies;2) We will ensure comprehensive annotation of reference genomes, including human, using the GO;3) We will support GO annotation efforts for emerging genomes and for those specialized sets of genes and proteins of particular community interest;and 4) We will provide annotations and tools to the research community thus supporting experimental biologists, genome informaticists, and computational biologists who are using GO annotations in their research particularly in the areas of functional genomics and comparative biology. The relevance of this work for public health is that comprehensive integration and standardization of biomedical and genomics information is an essential component of advancing the understanding of the molecular systems underlying human health and disease outcomes.